DCVoCamp2018

General

VoCamps are hands-on, working meetings where teams can spend some dedicated time creating lightweight vocabularies/ontologies for project use including publication on the Semantic Web. The emphasis is not to attempt to create the ultimate ontology in a particular domain, but to create integrated vocabularies with lightweight semantics supported by conceptual models that are good enough for people to start using them as published data on the Web. We seek clarified agreement & reduced ambiguities/ conflicts on scientific topics. Previous workshops have explored topics from the geospatial and earth sciences. The goal is to formally represent research phenomena using constrained & well engineered models to support understanding, reasoning & data interoperability. Part of the effort is creation of conceptual models and general patterns that provide a common framework to generate ontologies that are consistent and thus can support data interoperability.

We like data-grounded work since:

• Much of the utility of research ontologies will likely come from their ability to relate geospatial and other research data to other kinds of information.

The strategy of the session is to follow a "paper first, laptops second" format, where the modelling is done initially on paper and only later committed to formalization as ontology design patterns or ODPs.

For more see an overview of VoCamp methods and for an introduction to ontology design patterns and development methods see the briefing from prior DCVocamps or Ontology modeling with domain experts: The GeoVoCamp experience or Gary Berg-Cross's intro to GeoVocamps and overview of methods. For a slide overview of ODPs see Valentina Presutti's introduction and for an example of an ODP see A geo-ontology design pattern for semantic trajectories by Yingjie Hu et al

Where, When and How

Where

Events will kick off on Monday in the Natcher Building. NLM and NIH are accessible via the Metro Red line. 8600 Rockville Pike, Bethesda, MD 20894 (Note this is a late change from the peviously listed location of Lister Hill National Center for Biomedical Communications Board Room}

Details are now available from Evan Bolton (much thanks) Mon Oct 22

8:00AM – 9:00AM .. Arrival, coffee, etc. Natcher Building, (Bldg 45)/ Conference Rm A/B

9:00AM – 12:00PM .. meet as a group in Natcher Building, Bldg 45/ Conference Rm A/B (invited presentations, discussions)

12:00PM – 4:00PM .. break outs in Bldg 45/ Conference Rm A/B, Bldg45 Room G1, and Bldg45 Room G2

4:00PM – 5:30PM .. meet as a group in Bldg 45/ Conference Room A/B

Tue Oct 23

8:00AM – 9:00AM .. Arrival, coffee, etc. Bldg 45/Conference D

9:00AM – 10:00AM .. meet as a group in Bldg 45/Conference D

10:00AM – 4:00PM .. break outs in Bldg 45/Conference D, Bldg 45 Room J and Building 38A Conference room 3S

4:00PM – 5:30PM .. meet as a group in Bldg 45/Conference D

Wed Oct 24

8:00AM – 9:00AM .. Arrival, coffee, etc. Bldg 45/Conference D

9:00AM – 10:00AM .. meet as a group in Bldg 45/Conference D

10:00AM – 1:00PM .. break outs in Bldg 45/Conference D Room H & J

1:00PM – 3:00PM .. meet as a group in 45/Conference D

When

This year's VoCamp starts formally at 9 a.m. Monday Oct 22 and goes till 3 p.m. Wednesday Oct 24, 2018.

How Working Schedule

As in prior years we will meet the first morning as a group for short briefings on logistics, process and proposed topics. Usually this takes about 2 hours which is followed by a break. This will allow self organization into breakouts around 3 -4 Work Groups. Ideally these will be made up of domain experts, group facilitators and people with semantic/ontological experience.

often we have 1 or more remote presentations, as in the past, Our hosts will provided some remote access for these as part of the first morning sessions or at other general session times which are usually brief backs on status at the end of the day. Details on remote access will be provided a week before the workshop.

Individual topic groups may choose to have remote access for part of their meeting and we often have a distinguished researcher as a speaker to the whole on the 2nd or 3rd day as appropriate.

VoCamp Workshop Remote Access Info

Evan Bolton has provides the following information on access for the opening morning of the VoCamp:

   Monday, October 22, 2018
   9:00 am – 11am (EDT) | Eastern Daylight Time (New York, GMT-04:00)    
   https://nih.webex.com/nih
   Meeting number (access code): 629 467 200
   Meeting password: vocamp

Day 1 Monday Oct. 22nd

• 8 -9 Arrival and Coffee
• 9:00 - 9:30 Introductions, Welcome, Logistics & Schedule Overview –Note - Morning session includes a WebEx connect virtual meeting (Natcher Building Bldg 45/Conference Rm A/B  )
• 9:30 - 10:00 Workshop Vision, Schedule, Strategy, Methods, tools... - Gary Berg-Cross and others
• 10:00 -11:00 Working Topics (Presented by Topic Leaders)

 11:00- 11:15  Break

• 11:15 – 12:15 Group organization and introductions - setting goals, scope and process (In Breakout Rooms)

12:15 – 1:30  Lunch

• 1:30 – 4:00 Resume topic breakout meetings Concepts, Vocabulary and Models
• 4:00-5:30 Group Reports to the Whole – Natcher Building -Bldg45/Conference Rm A/B  ) Post 5:30 PM – Groups may make arrangements for dinner on their own

Day 2: Tuesday Oct. 23rd

• 9:00~9:45 Updates, Q & A Methods of the day etc. (schedule etc.) Main room (Natcher Building Bldg45/Conference Rm D )

• 9:45-10:45 Group Work on Competency Questions, connection terms to patterns (Breakout Rooms D and J)

~ 10:45 -11 Break

• 11:00-12:15 Group Work on Draft Models (Breakout Rooms)

12:15 -1:15 Lunch and Networking – on your own

• 1:15- 2:45 Work Groups – modeling choices & draft final conceptual model (Breakout Rooms)
• 2:45- 3:15 Work Groups identify data to test model & Prepare axioms for

initial formalizations

              3:15-3:30 Break    

• 3:30-4:30 Prepare Brief Back Report (Breakout Rooms)
• 4:30-5:30 Interim Group reports and discussion of Machine Learning as an Aid to ODP development Main Room (Broadcast as Virtual Meeting)

Dinner as organized by group interest

Day 3 Wednesday Oct. 24th

9:00-9:30 Updates, Q & A etc. (schedule, Tool advice etc.) Main Meeting Room 9:30-10:45 Work Groups Model Integration and alignments, Firming up products, check against data and competency questions (Breakout Rooms)

                   10:45-11:00 Break 

11:00-11:30 Prepare group reports and plans for follow up (Breakout Rooms)

12:00 -1:00 Group reports & Wrap up (Main Room) We expect to end with lunch options and allow people to travel as needed.

Our Topics

Note, briefings on these topic were presented and will be posted in the near future as our GitHub for this VoCamp is developed

Knowledge Model of ChemDB

A number of people including several from NIH such as Evan Bolton will be involved in this modeling effort.

Glaciers

This is a broad topic which a number of people have worked on as part of a virtual VoCamp. The intent is to follow up this prior work and polish off some of the models and vocaularies developed. Early work focused on entities and this work may include work on glacial processes and how these are affected by terrain. There is available data on glacier expansion and shrinkage, advances and retreats. While ontologies like ENVO capture some of these concepts they allow too shallow an understanding of how scientists view glaciers as systems that are influenced by a number of inputs and outputs.

Extending Hyfo to Glaciers

The Hydro Foundational Ontology or HyFo (Brodaric et al.,2016) is a domain reference ontology driven by foundational principles. It attempts to resolves some semantic heterogeneity issues of water bodies, as inclusive of it water matter, along with containment and spatial ideas. Each of these seems relevant to a frozen body of water such as a glacier and some effort will be focused on Tuesday to investigate this question as well as look out how HyFO and ENVO might be aligned.

Brodaric, Boyan, Torsten Hahmann, and Michael Gruninger. "An Ontological Analysis of Water Features." International Conference on GIScience Short Paper Proceedings. Vol. 1. No. 1. 2016.

Chem Safety

This may involve a follow up on the 2017 This session will follow up on prior work such as at the 2017 Vocamp on chemical process/safety/rxn patterns/chemical health & safety data issues. One particular idea is to integrate more closely with the large chemistry based datasets, such as PubChem and M/SDS. In addition, there are existing patterns that may be integrated to enhance the functionality of the core pattern and complete other pieces, such as QUDT16 for measurements and units, the ModifiedHazardous Material Pattern for modelling hazardous states, and the Material Transformation for extending ChemicalActivity.

Discussing Machine Learning as an Aid to ODP development

As part of discussions preparing for this VoCamp a number of us want pursue the idea of using one or more ML/text understanding Apps to try to extract info from relevant material on a topic of interest. We expect to set aside some time test the usefulness of this before and'during the session as a step to making this a best practice for future sessions. People may describe Apps for such a future attempt and what would be involved to actually employ such an approach.

Who - Organizers

1. Gary Berg-Cross (Ontolog and RDA) (general & local coordinator)
2. Evan Bolton PubChem (NCBI) (local coordinator)
3. Charles F. Vardeman (University of Notre Dame)
4. Torsten Hahmann (University of Maine)
5. Gaurav Sinha (Ohio University)
6. Leah McEwen (Cornell University)

"Registered" to Participate

1. Gary Berg-Cross (Ontolog and RDA) (general & local coordinator)
2. Evan Bolton PubChem (NCBI) (local coordinator)
3. Charles F. Vardeman (University of Notre Dame)
4. Hande Küçük-McGinty (Collaborative Drug Discovery)
5. Leah McEwen (Cornell University)
6. Cogan Shimizu (Wright State)
7. Torsten Hahmann (University of Maine) Tuesday only
8. Vinh Nguyen (NIH)
9. Patrick Stingley (CTO BLM)
10. Gaurav Sinha (Ohio University)

Some may have problems registering on this site. If you wish to register you can email Gary Berg-Cross using gbergcross at gmail dot com

Would Like to, but still uncertain

1. Gaurav Sinha (Ohio University)

Remote Participants

1. add your name here

Maps, Logistics

A map of NIH and its buildings is at: https://www.ors.od.nih.gov/maps/Pages/NIH-Visitor-Map.aspx Buildings 41 and 38A are at the bottom-right.

People need an ID to enter the NIH complex and this may take some time. See https://www.nih.gov/about-nih/visitor-information

Some may have problems registering on this site. If you wish to register you can email Gary Berg-Cross using gbergcross at gmail dot com

Dinning/Places to Eat

For civilized discussion we will likely have coffee and some snacks available. There are many options but lunch/breakfast is available on campus and via a walk to Bethesda if time permits. Check with local hosts. The Natcher Building has a cafeteria as a default.

Bethesda Hotels near NIH

See https://www.tripadvisor.com/Hotels-g41003-Bethesda_Montgomery_County_Maryland-Hotels.html

Ontological Humor

1. Can an occurrent and an endurant participate in events nicely?

1. What happens when sodium bicarbonate and vinegar meet in the Chem Safety bar?

1. Why did the n-gram cross the road?

1. What happened when a glacier snuggled with a alpine valley for a few decades?

1. Who got invited to the semantic science party?

1 - Yes, if they follow good axioms.

2. It is volcanic.

3. To ge to th ot si.

4. They formed a glaciarete.

5. Well Ontologies Defintely Participated (ODP).